# HG changeset patch
# User galaxyp
# Date 1615538466 0
# Node ID f522c08e900c9443cd3bde3b18d6227446191355
# Parent  37d669de28287c56901d1b638972188c19af9fcb
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"

diff -r 37d669de2828 -r f522c08e900c macros.xml
--- a/macros.xml	Fri Feb 19 21:24:41 2021 +0000
+++ b/macros.xml	Fri Mar 12 08:41:06 2021 +0000
@@ -65,7 +65,11 @@
                   cont_MYCO:
                   - MYCOPLASMA
                   - '1'
+                #if $search_opts.mbr.match_between_runs == 'True':
+                MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window}
+                #else:
                 MQpar_MatchingTimeWindow_num: 0.0
+                #end if
                 MatchBetweenRuns_wA: auto
                 MQpar_firstSearchTol_num: 20.0
                 firstSearch_outOfCalWarnSD_num: 2.0
diff -r 37d669de2828 -r f522c08e900c maxquant.xml
--- a/maxquant.xml	Fri Feb 19 21:24:41 2021 +0000
+++ b/maxquant.xml	Fri Mar 12 08:41:06 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy3">
+<tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy4">
     <macros>
         <xml name="output" token_format="tabular" token_label="default description" token_name="default">
             <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
@@ -89,7 +89,14 @@
             lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}
             lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}
             advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}
-            matchBetweenRuns: ${search_opts.match_between_runs}
+            matchBetweenRuns: ${search_opts.mbr.match_between_runs}
+            #if $search_opts.mbr.match_between_runs == 'True':
+            matchingTimeWindow: ${search_opts.mbr.matching_time_window}
+            matchingIonMobilityWindow: ${search_opts.mbr.matching_ion_mobility_window}
+            alignmentTimeWindow: ${search_opts.mbr.alignment_time_window}
+            alignmentIonMobilityWindow: ${search_opts.mbr.alignment_ion_mobility_window}
+            matchUnidentifiedFeatures: ${search_opts.mbr.match_unidentified_features}
+            #end if
             includeContaminants: ${search_opts.incl_contaminants}
             minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length}
             maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length}
@@ -223,7 +230,78 @@
                     - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
                     - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
                   #end if
-                #end if  
+                #end if
+                #if $pg.quant_method.select_quant_method == 'reporter_ion_ms3':
+                lcmsRunType: 'Reporter ion MS3'
+                reporterMassTolerance: 0.003
+                #if $pg.quant_method.filter_by_pif.filter_pif == 'True':
+                reporterPif: ${pg.quant_method.filter_by_pif.reporter_pif}
+                #else:
+                reporterPif: 0
+                #end if
+                reporterFraction: 0
+                reporterBasePeakRatio: 0
+                filterPif: ${pg.quant_method.filter_by_pif.filter_pif}
+                isobaricLabels:
+                  #if $pg.quant_method.iso_labels.labeling == 'custom':
+                    #for $l in $pg.quant_method.iso_labels.iso_label:
+                      - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
+                    #end for
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
+                    - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
+                    - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
+                    - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]
+                    - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
+                    - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
+                    - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
+                    - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
+                    - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
+                    - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]
+                    - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
+                    - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
+                    - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
+                    - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
+                    - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
+                    - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
+                    - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
+                    @TMT10PLEX@
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
+                    @TMT10PLEX@
+                    - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
+                    - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
+                    - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
+                  #end if
+                  #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
+                    - [iodoTMT6plex-Cys126,'',0,0,0,0,True]
+                    - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
+                    - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
+                    - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
+                    - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
+                    - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
+                  #end if
+                #end if
             #end for
         </configfile>
         <expand macro="ptxqc"/>
@@ -276,10 +354,29 @@
                    label="Calculate peak properties"
                    truevalue="True" falsevalue="False"
                    help="If checked, several quantities characterizing peaks and isotopes patterns are calculated. This may lead to a substantial increase in computation time."/>
-            <param name="match_between_runs" type="boolean" checked="false"
-                   label="Match between runs"
-                   truevalue="True" falsevalue="False"
-                   help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs."/>
+            <conditional name="mbr">
+                <param name="match_between_runs" type="select"
+                       label="Match between runs"
+                       help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs.">
+                    <option value="False" selected="true">No</option>
+                    <option value="True">Yes</option>
+                </param>
+                <when value="False"/>
+                <when value="True">
+                    <param name="matching_time_window" type="float" label="Match Time Window [min]" min="0" value="0.7"
+                       help="The time window that is used in 'Match between runs' for the transfer of identifications."/>
+                    <param name="matching_ion_mobility_window" type="float" label="Match Ion Mobility Window" min="0" value="0.05"
+                       help="The ion mobility window that is used in 'Match between runs' for the transfer of identifications."/>
+                    <param name="alignment_time_window" type="integer" label="Alignment Time Window [min]" min="0" value="20"
+                       help="The time window that is used in retention time alignment to search for the best alignment function."/>
+                    <param name="alignment_ion_mobility_window" type="integer" label="Alignment Ion Mobility" min="0" value="1"
+                       help="The ion mobility window that is used in ion mobility alignment to search for the best alignment function."/>
+                    <param name="match_unidentified_features" type="boolean" checked="false"
+                           label="Match unidentified Features"
+                           truevalue="True" falsevalue="False"
+                       help="Also unidentified peptide features will be matched between runs. Their expression profiles over multiple samples are written into the table called 'matchedFeatures.txt'."/>
+                </when>
+            </conditional>
             <param name="incl_contaminants" type="boolean" checked="true"
                    label="Include contaminants"
                    truevalue="True" falsevalue="False"
@@ -410,6 +507,7 @@
                     <option value="lfq">label free quantification</option>
                     <option value="silac">label based quantification</option>
                     <option value="reporter_ion_ms2">reporter ion MS2</option>
+                    <option value="reporter_ion_ms3">reporter ion MS3</option>
                 </param>
                 <when value=""/>
                 <when value="silac">
@@ -496,6 +594,60 @@
                         <when value="False"></when>
                     </conditional>
                 </when>
+                <when value="reporter_ion_ms3">
+                    <conditional name="iso_labels">
+                        <param name="labeling" type="select" label="isobaric labeling"
+                               help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
+                            <option value="custom">custom</option>
+                            <option value="tmt2plex">TMT2plex</option>
+                            <option value="tmt6plex">TMT6plex</option>
+                            <option value="tmt8plex">TMT8plex</option>
+                            <option value="tmt10plex">TMT10plex</option>
+                            <option value="tmt11plex">TMT11plex</option>
+                            <option value="itraq4plex">iTRAQ4plex</option>
+                            <option value="itraq8plex">iTRAQ8plex</option>
+                            <option value="iodotmt6plex">iodoTMT6plex</option>
+                        </param>
+
+                        <when value="tmt2plex"></when>
+                        <when value="tmt6plex"></when>
+                        <when value="tmt8plex"></when>
+                        <when value="tmt10plex"></when>
+                        <when value="tmt11plex"></when>
+                        <when value="itraq4plex"></when>
+                        <when value="itraq8plex"></when>
+                        <when value="iodotmt6plex"></when>
+                        <when value="custom">
+                            <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
+                                <param name="internallabel" type="select" label="internal label" help="contains Lys">
+                                    <expand macro="iso_labels"/>
+                                </param>
+                                <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
+                                    <option value="">None</option>
+                                    <expand macro="iso_labels"/>
+                                </param>
+                                <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
+                                <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
+                                <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
+                                <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
+                                <param type="boolean" name="tmtlike" checked="false"
+                                       label="TMT-like"
+                                       truevalue="True" falsevalue="False"/>
+                            </repeat>
+                        </when>
+                    </conditional>
+                    <conditional name="filter_by_pif">
+                        <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"
+                               truevalue="True" falsevalue="False"
+                               help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>
+                        <when value="True">
+                            <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
+                                   max="1"
+                                   help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
+                        </when>
+                        <when value="False"></when>
+                    </conditional>
+                </when>
             </conditional>
         </repeat>
 
@@ -632,6 +784,82 @@
             <!-- high difference due to unconsistant xml formatting in MQ -->
             <output name="mqpar" file="02/mqpar.xml" lines_diff="24" />
         </test>
+        <!-- reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only -->
+        <test expect_num_outputs="3">
+            <param name="ftype" value=".mzxml" />
+            <param name="fasta_files" value="bsa.fasta" />
+            <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
+            <param name="description_parse_rule" value="&gt;(.*)" />
+            <param name="incl_contaminants" value="False" /> <!-- non-default value -->
+            <param name="min_pep_length" value="7" /> <!-- non-default value -->
+            <param name="max_pep_length" value="24" /> <!-- non-default value -->
+            <param name="decoy_mode" value="randomize" /> <!-- non-default value -->
+            <param name="psm_fdr" value="0.5" /> <!-- non-default value -->
+            <param name="protein_fdr" value="0.4" /> <!-- non-default value -->
+            <section name="protein_quant">
+                <param name="peptides_for_quantification" value="0"/><!-- non-default value -->
+                <conditional name="only_unmod_prot">
+                    <param name="unmod_prot" value="True"/>
+                    <param name="mods_used_prot_quant" value="Pro5,Pro6"/>
+                </conditional>
+            </section>
+            <repeat name="paramGroups">
+                <param name="files" value="BSA_min_23.mzXML"/>
+                <param name="variableModifications" value="Oxidation (M)" />
+                <param name="fixedModifications" value="" />
+                <conditional name="quant_method">
+                    <param name="select_quant_method" value="reporter_ion_ms3" />
+                    <conditional name="iso_labels">
+                        <param name="labeling" value="custom" />
+                        <repeat name="iso_label">
+                            <param name="internallabel" value="TMT2plex-Lys126" />
+                            <param name="terminallabel" value="TMT2plex-Nter126" />
+                            <param name="tmtlike" value="True" />
+                            <param name="cp1" value="6.7" />
+                            <param name="cp2" value="3" />
+                        </repeat>
+                        <repeat name="iso_label">
+                            <param name="internallabel" value="TMT2plex-Lys127" />
+                            <param name="terminallabel" value="TMT2plex-Nter127" />
+                            <param name="tmtlike" value="True" />
+                        </repeat>
+                    </conditional>
+                    <conditional name="filter_by_pif">
+                        <param name="filter_pif" value="False"/>
+                        <param name="reporter_pif"
+                               value="0.6"/> <!-- as filter_pif is False this value will be ignored and 0 used instead -->
+                    </conditional>
+                </conditional>
+            </repeat>
+            <repeat name="paramGroups">
+                <param name="files" value="BSA_min_22"/>
+                <param name="variableModifications" value="" />
+                <param name="fixedModifications" value="" />
+                <param name="enzymes" value="" />
+                <conditional name="quant_method">
+                    <param name="select_quant_method" value="reporter_ion_ms3"/>
+                    <conditional name="iso_labels">
+                        <param name="labeling" value="itraq4plex"/>
+                    </conditional>
+                    <conditional name="filter_by_pif">
+                        <param name="filter_pif" value="True"/>
+                        <param name="reporter_pif" value="0.8"/> <!-- as filter_pif is True this value is used -->
+                    </conditional>
+                </conditional>
+            </repeat>
+            <param name="dry_run" value="True" />
+            <param name="output" value="config,mqpar,mzTab" />
+            <output name="config" file="06/config.yml" lines_diff="2">
+                <assert_contents>
+                    <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" />
+                </assert_contents>
+            </output>
+            <output name="mqpar" file="06/mqpar.xml" lines_diff="6">
+                <assert_contents>
+                    <has_text_matching expression=".lcmsRunType.Reporter ion MS3.\/lcmsRunType." />
+                </assert_contents>
+            </output>
+        </test>
         <!-- lfq, testing yaml conf file and mqpar.xml only -->
         <test expect_num_outputs="2">
             <param name="ftype" value=".mzxml" />
@@ -654,6 +882,37 @@
             <output name="config" file="03/config.yml" lines_diff="2" />
             <output name="mqpar" file="03/mqpar.xml" lines_diff="10" />
         </test>
+        <!-- Test for MBR -->
+        <test expect_num_outputs="2">
+            <param name="ftype" value=".mzxml" />
+            <param name="fasta_files" value="bsa.fasta" />
+            <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
+            <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
+            <param name="min_unique_pep" value="1" />
+            <param name="ibaq" value="True" />
+            <param name="match_between_runs" value="True" />
+            <param name="ibaqLogFit" value="False" />
+            <repeat name="paramGroups">
+                <param name="files" value="BSA_min_22"/>
+                <param name="maxMissedCleavages" value="1"/>
+                <param name="variableModifications" value="Oxidation (M)" />
+                <conditional name="quant_method">
+                    <param name="select_quant_method" value="lfq" />
+                </conditional>
+            </repeat>
+            <param name="dry_run" value="True" />
+            <param name="output" value="config,mqpar" />
+            <output name="config" file="05/config.yml" lines_diff="2">
+                <assert_contents>
+                    <has_text_matching expression="matchBetweenRuns\: True" />
+                </assert_contents>
+            </output>
+            <output name="mqpar" file="05/mqpar.xml" lines_diff="4">
+                <assert_contents>
+                    <has_text_matching expression=".matchBetweenRuns.True.\/matchBetweenRuns." />
+                </assert_contents>
+            </output>
+        </test>
         <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only -->
         <test expect_num_outputs="2">
             <param name="ftype" value=".mzxml" />
@@ -744,7 +1003,7 @@
 
         - for two channels: choose options from light and heavy sections
         - for three channels: choose options from light, medium and heavy sections
-    - reporter ion ms2: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling
+    - reporter ion ms2/ms3: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling
 - PTXQC quality control: quality control software creates an automatic quality control pdf report 
 
 
diff -r 37d669de2828 -r f522c08e900c test-data/05/config.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/05/config.yml	Fri Mar 12 08:41:06 2021 +0000
@@ -0,0 +1,45 @@
+
+            fastaFiles: [/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat]
+            parseRules:
+              identifierParseRule: '^>.*\|(.*)\|.*$'
+              descriptionParseRule: '^>.*\|.*\|[^ ]+ (.*) OS.*$'
+            minUniquePeptides: 1
+            minPepLen: 7
+            maxPeptideMass: 4600
+            calcPeakProperties: False
+            writeMzTab: False
+            ibaq: True
+            ibaqLogFit: False
+            separateLfq: False
+            lfqStabilizeLargeRatios: True
+            lfqRequireMsms: True
+            advancedSiteIntensities: True
+            matchBetweenRuns: True
+            matchingTimeWindow: 0.7
+            matchingIonMobilityWindow: 0.05
+            alignmentTimeWindow: 20
+            alignmentIonMobilityWindow: 1
+            matchUnidentifiedFeatures: False
+            includeContaminants: True
+            minPeptideLengthForUnspecificSearch: 8
+            maxPeptideLengthForUnspecificSearch: 25
+            decoyMode: revert
+            peptideFdr: 0.01
+            proteinFdr: 0.01
+            quantMode: 1
+            restrictProteinQuantification: True
+            restrictMods: [Oxidation (M),Acetyl (Protein N-term)]
+            useCounterparts: True
+            paramGroups:
+              - files: ['BSA_min_22.mzxml']
+                maxMissedCleavages: 1
+                fixedModifications: [Carbamidomethyl (C)]
+                variableModifications: [Oxidation (M)]
+                enzymes: [Trypsin/P]
+                enzymeMode: 0
+                lfqMode: 1
+                lfqSkipNorm: True
+                lfqMinEdgesPerNode: 3
+                lfqAvEdgesPerNode: 6
+                lfqMinRatioCount: 2
+        
\ No newline at end of file
diff -r 37d669de2828 -r f522c08e900c test-data/05/mqpar.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/05/mqpar.xml	Fri Mar 12 08:41:06 2021 +0000
@@ -0,0 +1,451 @@
+<?xml version="1.0" ?>
+<MaxQuantParams>
+	<fastaFiles>
+		<FastaFileInfo>
+			<fastaFilePath>/tmp/tmp0wswhy4o/files/4/7/7/dataset_4770959a-66d4-405f-a5b5-48d25389063a.dat</fastaFilePath>
+			<identifierParseRule>^&gt;.*\|(.*)\|.*$</identifierParseRule>
+			<descriptionParseRule>^&gt;.*\|.*\|[^ ]+ (.*) OS.*$</descriptionParseRule>
+			<taxonomyParseRule/>
+			<variationParseRule/>
+			<modificationParseRule/>
+			<taxonomyId/>
+		</FastaFileInfo>
+	</fastaFiles>
+	<fastaFilesProteogenomics>
+   </fastaFilesProteogenomics>
+	<fastaFilesFirstSearch>
+   </fastaFilesFirstSearch>
+	<fixedSearchFolder/>
+	<andromedaCacheSize>350000</andromedaCacheSize>
+	<advancedRatios>True</advancedRatios>
+	<pvalThres>0.005</pvalThres>
+	<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
+	<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
+	<rtShift>False</rtShift>
+	<separateLfq>False</separateLfq>
+	<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
+	<lfqRequireMsms>True</lfqRequireMsms>
+	<decoyMode>revert</decoyMode>
+	<boxCarMode>all</boxCarMode>
+	<includeContaminants>True</includeContaminants>
+	<maxPeptideMass>4600</maxPeptideMass>
+	<epsilonMutationScore>True</epsilonMutationScore>
+	<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
+	<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
+	<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
+	<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
+	<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
+	<minScoreModifiedPeptides>40</minScoreModifiedPeptides>
+	<secondPeptide>True</secondPeptide>
+	<matchBetweenRuns>True</matchBetweenRuns>
+	<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
+	<matchBetweenRunsFdr>False</matchBetweenRunsFdr>
+	<dependentPeptides>False</dependentPeptides>
+	<dependentPeptideFdr>0</dependentPeptideFdr>
+	<dependentPeptideMassBin>0</dependentPeptideMassBin>
+	<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
+	<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
+	<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
+	<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
+	<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
+	<msmsConnection>False</msmsConnection>
+	<ibaq>True</ibaq>
+	<top3>False</top3>
+	<independentEnzymes>False</independentEnzymes>
+	<useDeltaScore>False</useDeltaScore>
+	<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
+	<taxonomyLevel>Species</taxonomyLevel>
+	<avalon>False</avalon>
+	<nModColumns>3</nModColumns>
+	<ibaqLogFit>False</ibaqLogFit>
+	<razorProteinFdr>True</razorProteinFdr>
+	<deNovoSequencing>False</deNovoSequencing>
+	<deNovoVarMods>True</deNovoVarMods>
+	<massDifferenceSearch>False</massDifferenceSearch>
+	<isotopeCalc>False</isotopeCalc>
+	<writePeptidesForSpectrumFile/>
+	<intensityPredictionsFile>
+   </intensityPredictionsFile>
+	<minPepLen>7</minPepLen>
+	<psmFdrCrosslink>0.01</psmFdrCrosslink>
+	<peptideFdr>0.01</peptideFdr>
+	<proteinFdr>0.01</proteinFdr>
+	<siteFdr>0.01</siteFdr>
+	<minPeptideLengthForUnspecificSearch>8</minPeptideLengthForUnspecificSearch>
+	<maxPeptideLengthForUnspecificSearch>25</maxPeptideLengthForUnspecificSearch>
+	<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
+	<minPeptides>1</minPeptides>
+	<minRazorPeptides>1</minRazorPeptides>
+	<minUniquePeptides>1</minUniquePeptides>
+	<useCounterparts>True</useCounterparts>
+	<advancedSiteIntensities>True</advancedSiteIntensities>
+	<customProteinQuantification>False</customProteinQuantification>
+	<customProteinQuantificationFile/>
+	<minRatioCount>2</minRatioCount>
+	<restrictProteinQuantification>True</restrictProteinQuantification>
+	<restrictMods>
+		<string>Oxidation (M)</string>
+		<string>Acetyl (Protein N-term)</string>
+	</restrictMods>
+	<matchingTimeWindow>0.7</matchingTimeWindow>
+	<matchingIonMobilityWindow>0.05</matchingIonMobilityWindow>
+	<alignmentTimeWindow>20</alignmentTimeWindow>
+	<alignmentIonMobilityWindow>1</alignmentIonMobilityWindow>
+	<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
+	<compositionPrediction>0</compositionPrediction>
+	<quantMode>1</quantMode>
+	<massDifferenceMods>
+   </massDifferenceMods>
+	<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
+	<writeMsScansTable>False</writeMsScansTable>
+	<writeMsmsScansTable>True</writeMsmsScansTable>
+	<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
+	<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
+	<writeMs3ScansTable>True</writeMs3ScansTable>
+	<writeAllPeptidesTable>True</writeAllPeptidesTable>
+	<writeMzRangeTable>True</writeMzRangeTable>
+	<writeMzTab>False</writeMzTab>
+	<disableMd5>False</disableMd5>
+	<cacheBinInds>True</cacheBinInds>
+	<etdIncludeB>False</etdIncludeB>
+	<ms2PrecursorShift>0</ms2PrecursorShift>
+	<complementaryIonPpm>20</complementaryIonPpm>
+	<variationParseRule/>
+	<variationMode>none</variationMode>
+	<useSeriesReporters>False</useSeriesReporters>
+	<name>templateSession</name>
+	<maxQuantVersion>1.6.10.43</maxQuantVersion>
+	<tempFolder/>
+	<pluginFolder/>
+	<numThreads>1</numThreads>
+	<emailAddress/>
+	<smtpHost/>
+	<emailFromAddress/>
+	<fixedCombinedFolder/>
+	<fullMinMz>-1.79769313486232E+308</fullMinMz>
+	<fullMaxMz>1.79769313486232E+308</fullMaxMz>
+	<sendEmail>False</sendEmail>
+	<ionCountIntensities>False</ionCountIntensities>
+	<verboseColumnHeaders>False</verboseColumnHeaders>
+	<calcPeakProperties>False</calcPeakProperties>
+	<showCentroidMassDifferences>False</showCentroidMassDifferences>
+	<showIsotopeMassDifferences>False</showIsotopeMassDifferences>
+	<useDotNetCore>False</useDotNetCore>
+	<filePaths>
+		<string>/tmp/tmp0wswhy4o/job_working_directory/000/7/working/BSA_min_22.mzxml</string>
+	</filePaths>
+	<experiments>
+		<string>BSA_min_22.mzxml</string>
+	</experiments>
+	<fractions>
+		<short>32767</short>
+	</fractions>
+	<ptms>
+		<boolean>False</boolean>
+	</ptms>
+	<paramGroupIndices>
+		<int>0</int>
+	</paramGroupIndices>
+	<referenceChannel>
+		<string/>
+	</referenceChannel>
+	<intensPred>False</intensPred>
+	<intensPredModelReTrain>False</intensPredModelReTrain>
+	<parameterGroups>
+		<parameterGroup>
+			<msInstrument>0</msInstrument>
+			<maxCharge>7</maxCharge>
+			<minPeakLen>2</minPeakLen>
+			<diaMinPeakLen>2</diaMinPeakLen>
+			<useMs1Centroids>False</useMs1Centroids>
+			<useMs2Centroids>False</useMs2Centroids>
+			<cutPeaks>True</cutPeaks>
+			<gapScans>1</gapScans>
+			<minTime>NaN</minTime>
+			<maxTime>NaN</maxTime>
+			<matchType>MatchFromAndTo</matchType>
+			<intensityDetermination>0</intensityDetermination>
+			<centroidMatchTol>8</centroidMatchTol>
+			<centroidMatchTolInPpm>True</centroidMatchTolInPpm>
+			<centroidHalfWidth>35</centroidHalfWidth>
+			<centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
+			<valleyFactor>1.4</valleyFactor>
+			<isotopeValleyFactor>1.2</isotopeValleyFactor>
+			<advancedPeakSplitting>False</advancedPeakSplitting>
+			<intensityThreshold>0</intensityThreshold>
+			<labelMods>
+				<string/>
+			</labelMods>
+			<lcmsRunType>Standard</lcmsRunType>
+			<reQuantify>False</reQuantify>
+			<lfqMode>1</lfqMode>
+			<lfqSkipNorm>True</lfqSkipNorm>
+			<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
+			<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
+			<lfqMaxFeatures>100000</lfqMaxFeatures>
+			<neucodeMaxPpm>0</neucodeMaxPpm>
+			<neucodeResolution>0</neucodeResolution>
+			<neucodeResolutionInMda>False</neucodeResolutionInMda>
+			<neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
+			<fastLfq>True</fastLfq>
+			<lfqRestrictFeatures>False</lfqRestrictFeatures>
+			<lfqMinRatioCount>2</lfqMinRatioCount>
+			<maxLabeledAa>0</maxLabeledAa>
+			<maxNmods>5</maxNmods>
+			<maxMissedCleavages>1</maxMissedCleavages>
+			<multiplicity>1</multiplicity>
+			<enzymeMode>0</enzymeMode>
+			<complementaryReporterType>0</complementaryReporterType>
+			<reporterNormalization>0</reporterNormalization>
+			<neucodeIntensityMode>0</neucodeIntensityMode>
+			<fixedModifications>
+				<string>Carbamidomethyl (C)</string>
+			</fixedModifications>
+			<enzymes>
+				<string>Trypsin/P</string>
+			</enzymes>
+			<enzymesFirstSearch>
+         </enzymesFirstSearch>
+			<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
+			<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
+			<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
+			<variableModifications>
+				<string>Oxidation (M)</string>
+			</variableModifications>
+			<useMultiModification>False</useMultiModification>
+			<multiModifications>
+         </multiModifications>
+			<isobaricLabels>
+         </isobaricLabels>
+			<neucodeLabels>
+         </neucodeLabels>
+			<variableModificationsFirstSearch>
+         </variableModificationsFirstSearch>
+			<hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
+			<additionalVariableModifications>
+         </additionalVariableModifications>
+			<additionalVariableModificationProteins>
+         </additionalVariableModificationProteins>
+			<doMassFiltering>True</doMassFiltering>
+			<firstSearchTol>20</firstSearchTol>
+			<mainSearchTol>4.5</mainSearchTol>
+			<searchTolInPpm>True</searchTolInPpm>
+			<isotopeMatchTol>2</isotopeMatchTol>
+			<isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
+			<isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
+			<theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
+			<checkMassDeficit>True</checkMassDeficit>
+			<recalibrationInPpm>True</recalibrationInPpm>
+			<intensityDependentCalibration>False</intensityDependentCalibration>
+			<minScoreForCalibration>70</minScoreForCalibration>
+			<matchLibraryFile>False</matchLibraryFile>
+			<libraryFile/>
+			<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
+			<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
+			<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
+			<reporterMassTolerance>NaN</reporterMassTolerance>
+			<reporterPif>NaN</reporterPif>
+			<filterPif>False</filterPif>
+			<reporterFraction>NaN</reporterFraction>
+			<reporterBasePeakRatio>NaN</reporterBasePeakRatio>
+			<timsHalfWidth>0</timsHalfWidth>
+			<timsStep>0</timsStep>
+			<timsResolution>0</timsResolution>
+			<timsMinMsmsIntensity>0</timsMinMsmsIntensity>
+			<timsRemovePrecursor>True</timsRemovePrecursor>
+			<timsIsobaricLabels>False</timsIsobaricLabels>
+			<timsCollapseMsms>True</timsCollapseMsms>
+			<crosslinkSearch>False</crosslinkSearch>
+			<crossLinker/>
+			<minMatchXl>0</minMatchXl>
+			<minPairedPepLenXl>6</minPairedPepLenXl>
+			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
+			<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
+			<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
+			<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
+			<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
+			<crosslinkModifications>
+         </crosslinkModifications>
+			<crosslinkFastaFiles>
+         </crosslinkFastaFiles>
+			<crosslinkSites>
+         </crosslinkSites>
+			<crosslinkNetworkFiles>
+         </crosslinkNetworkFiles>
+			<crosslinkMode/>
+			<peakRefinement>False</peakRefinement>
+			<isobaricSumOverWindow>True</isobaricSumOverWindow>
+			<isobaricWeightExponent>0.75</isobaricWeightExponent>
+			<diaLibraryType>0</diaLibraryType>
+			<diaLibraryPath/>
+			<diaPeptidePaths>
+         </diaPeptidePaths>
+			<diaEvidencePaths>
+         </diaEvidencePaths>
+			<diaMsmsPaths>
+         </diaMsmsPaths>
+			<diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
+			<diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
+			<diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
+			<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
+			<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
+			<diaScoreN>7</diaScoreN>
+			<diaMinScore>2.99</diaMinScore>
+			<diaPrecursorQuant>False</diaPrecursorQuant>
+			<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
+		</parameterGroup>
+	</parameterGroups>
+	<msmsParamsArray>
+		<msmsParams>
+			<Name>FTMS</Name>
+			<MatchTolerance>20</MatchTolerance>
+			<MatchToleranceInPpm>True</MatchToleranceInPpm>
+			<DeisotopeTolerance>7</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>10</DeNovoTolerance>
+			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
+			<Deisotope>True</Deisotope>
+			<Topx>12</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+		<msmsParams>
+			<Name>ITMS</Name>
+			<MatchTolerance>0.5</MatchTolerance>
+			<MatchToleranceInPpm>False</MatchToleranceInPpm>
+			<DeisotopeTolerance>0.15</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>0.25</DeNovoTolerance>
+			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+			<Deisotope>False</Deisotope>
+			<Topx>8</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+		<msmsParams>
+			<Name>TOF</Name>
+			<MatchTolerance>40</MatchTolerance>
+			<MatchToleranceInPpm>True</MatchToleranceInPpm>
+			<DeisotopeTolerance>0.01</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>0.02</DeNovoTolerance>
+			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+			<Deisotope>True</Deisotope>
+			<Topx>10</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+		<msmsParams>
+			<Name>Unknown</Name>
+			<MatchTolerance>20</MatchTolerance>
+			<MatchToleranceInPpm>True</MatchToleranceInPpm>
+			<DeisotopeTolerance>7</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>10</DeNovoTolerance>
+			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
+			<Deisotope>True</Deisotope>
+			<Topx>12</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+	</msmsParamsArray>
+	<fragmentationParamsArray>
+		<fragmentationParams>
+			<Name>CID</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>HCD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>ETD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>PQD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>ETHCD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>ETCID</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>UVPD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>Unknown</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+	</fragmentationParamsArray>
+</MaxQuantParams>
+
diff -r 37d669de2828 -r f522c08e900c test-data/06/config.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/06/config.yml	Fri Mar 12 08:41:06 2021 +0000
@@ -0,0 +1,59 @@
+
+            fastaFiles: [/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat]
+            parseRules:
+              identifierParseRule: '>([^\s]*)'
+              descriptionParseRule: '>(.*)'
+            minUniquePeptides: 0
+            minPepLen: 7
+            maxPeptideMass: 4600
+            calcPeakProperties: False
+            writeMzTab: True
+            separateLfq: False
+            lfqStabilizeLargeRatios: True
+            lfqRequireMsms: True
+            advancedSiteIntensities: True
+            matchBetweenRuns: False
+            includeContaminants: False
+            minPeptideLengthForUnspecificSearch: 7
+            maxPeptideLengthForUnspecificSearch: 24
+            decoyMode: randomize
+            peptideFdr: 0.5
+            proteinFdr: 0.4
+            quantMode: 0
+            restrictProteinQuantification: True
+            restrictMods: [Pro5,Pro6]
+            useCounterparts: True
+            paramGroups:
+              - files: ['BSA_min_23.mzXML']
+                maxMissedCleavages: 2
+                fixedModifications: []
+                variableModifications: [Oxidation (M)]
+                enzymes: [Trypsin/P]
+                enzymeMode: 0
+                lcmsRunType: 'Reporter ion MS3'
+                reporterMassTolerance: 0.003
+                reporterPif: 0
+                reporterFraction: 0
+                reporterBasePeakRatio: 0
+                filterPif: False
+                isobaricLabels:
+                      - ['TMT2plex-Lys126','TMT2plex-Nter126',0.0,0.0,6.7,3.0,True]
+                      - ['TMT2plex-Lys127','TMT2plex-Nter127',0.0,0.0,0.0,0.0,True]
+              - files: ['BSA_min_22.mzxml']
+                maxMissedCleavages: 2
+                fixedModifications: []
+                variableModifications: []
+                enzymes: []
+                enzymeMode: 0
+                lcmsRunType: 'Reporter ion MS3'
+                reporterMassTolerance: 0.003
+                reporterPif: 0.8
+                reporterFraction: 0
+                reporterBasePeakRatio: 0
+                filterPif: True
+                isobaricLabels:
+                    - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
+                    - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
+        
\ No newline at end of file
diff -r 37d669de2828 -r f522c08e900c test-data/06/mqpar.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/06/mqpar.xml	Fri Mar 12 08:41:06 2021 +0000
@@ -0,0 +1,645 @@
+<?xml version="1.0" ?>
+<MaxQuantParams>
+	<fastaFiles>
+		<FastaFileInfo>
+			<fastaFilePath>/tmp/tmp0wswhy4o/files/e/e/e/dataset_eee05aed-87d2-4635-87b0-dd7930cc43dc.dat</fastaFilePath>
+			<identifierParseRule>&gt;([^\s]*)</identifierParseRule>
+			<descriptionParseRule>&gt;(.*)</descriptionParseRule>
+			<taxonomyParseRule/>
+			<variationParseRule/>
+			<modificationParseRule/>
+			<taxonomyId/>
+		</FastaFileInfo>
+	</fastaFiles>
+	<fastaFilesProteogenomics>
+   </fastaFilesProteogenomics>
+	<fastaFilesFirstSearch>
+   </fastaFilesFirstSearch>
+	<fixedSearchFolder/>
+	<andromedaCacheSize>350000</andromedaCacheSize>
+	<advancedRatios>True</advancedRatios>
+	<pvalThres>0.005</pvalThres>
+	<neucodeRatioBasedQuantification>False</neucodeRatioBasedQuantification>
+	<neucodeStabilizeLargeRatios>False</neucodeStabilizeLargeRatios>
+	<rtShift>False</rtShift>
+	<separateLfq>False</separateLfq>
+	<lfqStabilizeLargeRatios>True</lfqStabilizeLargeRatios>
+	<lfqRequireMsms>True</lfqRequireMsms>
+	<decoyMode>randomize</decoyMode>
+	<boxCarMode>all</boxCarMode>
+	<includeContaminants>False</includeContaminants>
+	<maxPeptideMass>4600</maxPeptideMass>
+	<epsilonMutationScore>True</epsilonMutationScore>
+	<mutatedPeptidesSeparately>True</mutatedPeptidesSeparately>
+	<proteogenomicPeptidesSeparately>True</proteogenomicPeptidesSeparately>
+	<minDeltaScoreUnmodifiedPeptides>0</minDeltaScoreUnmodifiedPeptides>
+	<minDeltaScoreModifiedPeptides>6</minDeltaScoreModifiedPeptides>
+	<minScoreUnmodifiedPeptides>0</minScoreUnmodifiedPeptides>
+	<minScoreModifiedPeptides>40</minScoreModifiedPeptides>
+	<secondPeptide>True</secondPeptide>
+	<matchBetweenRuns>False</matchBetweenRuns>
+	<matchUnidentifiedFeatures>False</matchUnidentifiedFeatures>
+	<matchBetweenRunsFdr>False</matchBetweenRunsFdr>
+	<dependentPeptides>False</dependentPeptides>
+	<dependentPeptideFdr>0</dependentPeptideFdr>
+	<dependentPeptideMassBin>0</dependentPeptideMassBin>
+	<dependentPeptidesBetweenRuns>False</dependentPeptidesBetweenRuns>
+	<dependentPeptidesWithinExperiment>False</dependentPeptidesWithinExperiment>
+	<dependentPeptidesWithinParameterGroup>False</dependentPeptidesWithinParameterGroup>
+	<dependentPeptidesRestrictFractions>False</dependentPeptidesRestrictFractions>
+	<dependentPeptidesFractionDifference>0</dependentPeptidesFractionDifference>
+	<msmsConnection>False</msmsConnection>
+	<ibaq>False</ibaq>
+	<top3>False</top3>
+	<independentEnzymes>False</independentEnzymes>
+	<useDeltaScore>False</useDeltaScore>
+	<splitProteinGroupsByTaxonomy>False</splitProteinGroupsByTaxonomy>
+	<taxonomyLevel>Species</taxonomyLevel>
+	<avalon>False</avalon>
+	<nModColumns>3</nModColumns>
+	<ibaqLogFit>False</ibaqLogFit>
+	<razorProteinFdr>True</razorProteinFdr>
+	<deNovoSequencing>False</deNovoSequencing>
+	<deNovoVarMods>True</deNovoVarMods>
+	<massDifferenceSearch>False</massDifferenceSearch>
+	<isotopeCalc>False</isotopeCalc>
+	<writePeptidesForSpectrumFile/>
+	<intensityPredictionsFile>
+   </intensityPredictionsFile>
+	<minPepLen>7</minPepLen>
+	<psmFdrCrosslink>0.01</psmFdrCrosslink>
+	<peptideFdr>0.5</peptideFdr>
+	<proteinFdr>0.4</proteinFdr>
+	<siteFdr>0.01</siteFdr>
+	<minPeptideLengthForUnspecificSearch>7</minPeptideLengthForUnspecificSearch>
+	<maxPeptideLengthForUnspecificSearch>24</maxPeptideLengthForUnspecificSearch>
+	<useNormRatiosForOccupancy>True</useNormRatiosForOccupancy>
+	<minPeptides>1</minPeptides>
+	<minRazorPeptides>1</minRazorPeptides>
+	<minUniquePeptides>0</minUniquePeptides>
+	<useCounterparts>True</useCounterparts>
+	<advancedSiteIntensities>True</advancedSiteIntensities>
+	<customProteinQuantification>False</customProteinQuantification>
+	<customProteinQuantificationFile/>
+	<minRatioCount>2</minRatioCount>
+	<restrictProteinQuantification>True</restrictProteinQuantification>
+	<restrictMods>
+		<string>Pro5</string>
+		<string>Pro6</string>
+	</restrictMods>
+	<matchingTimeWindow>0</matchingTimeWindow>
+	<matchingIonMobilityWindow>0</matchingIonMobilityWindow>
+	<alignmentTimeWindow>0</alignmentTimeWindow>
+	<alignmentIonMobilityWindow>0</alignmentIonMobilityWindow>
+	<numberOfCandidatesMsms>15</numberOfCandidatesMsms>
+	<compositionPrediction>0</compositionPrediction>
+	<quantMode>0</quantMode>
+	<massDifferenceMods>
+   </massDifferenceMods>
+	<mainSearchMaxCombinations>200</mainSearchMaxCombinations>
+	<writeMsScansTable>False</writeMsScansTable>
+	<writeMsmsScansTable>True</writeMsmsScansTable>
+	<writePasefMsmsScansTable>True</writePasefMsmsScansTable>
+	<writeAccumulatedPasefMsmsScansTable>True</writeAccumulatedPasefMsmsScansTable>
+	<writeMs3ScansTable>True</writeMs3ScansTable>
+	<writeAllPeptidesTable>True</writeAllPeptidesTable>
+	<writeMzRangeTable>True</writeMzRangeTable>
+	<writeMzTab>True</writeMzTab>
+	<disableMd5>False</disableMd5>
+	<cacheBinInds>True</cacheBinInds>
+	<etdIncludeB>False</etdIncludeB>
+	<ms2PrecursorShift>0</ms2PrecursorShift>
+	<complementaryIonPpm>20</complementaryIonPpm>
+	<variationParseRule/>
+	<variationMode>none</variationMode>
+	<useSeriesReporters>False</useSeriesReporters>
+	<name>templateSession</name>
+	<maxQuantVersion>1.6.10.43</maxQuantVersion>
+	<tempFolder/>
+	<pluginFolder/>
+	<numThreads>1</numThreads>
+	<emailAddress/>
+	<smtpHost/>
+	<emailFromAddress/>
+	<fixedCombinedFolder/>
+	<fullMinMz>-1.79769313486232E+308</fullMinMz>
+	<fullMaxMz>1.79769313486232E+308</fullMaxMz>
+	<sendEmail>False</sendEmail>
+	<ionCountIntensities>False</ionCountIntensities>
+	<verboseColumnHeaders>False</verboseColumnHeaders>
+	<calcPeakProperties>False</calcPeakProperties>
+	<showCentroidMassDifferences>False</showCentroidMassDifferences>
+	<showIsotopeMassDifferences>False</showIsotopeMassDifferences>
+	<useDotNetCore>False</useDotNetCore>
+	<filePaths>
+		<string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_23.mzXML</string>
+		<string>/tmp/tmp0wswhy4o/job_working_directory/000/4/working/BSA_min_22.mzxml</string>
+	</filePaths>
+	<experiments>
+		<string>BSA_min_23.mzXML</string>
+		<string>BSA_min_22.mzxml</string>
+	</experiments>
+	<fractions>
+		<short>32767</short>
+		<short>32767</short>
+	</fractions>
+	<ptms>
+		<boolean>False</boolean>
+		<boolean>False</boolean>
+	</ptms>
+	<paramGroupIndices>
+		<int>0</int>
+		<int>1</int>
+	</paramGroupIndices>
+	<referenceChannel>
+		<string/>
+		<string/>
+	</referenceChannel>
+	<intensPred>False</intensPred>
+	<intensPredModelReTrain>False</intensPredModelReTrain>
+	<parameterGroups>
+		<parameterGroup>
+			<msInstrument>0</msInstrument>
+			<maxCharge>7</maxCharge>
+			<minPeakLen>2</minPeakLen>
+			<diaMinPeakLen>2</diaMinPeakLen>
+			<useMs1Centroids>False</useMs1Centroids>
+			<useMs2Centroids>False</useMs2Centroids>
+			<cutPeaks>True</cutPeaks>
+			<gapScans>1</gapScans>
+			<minTime>NaN</minTime>
+			<maxTime>NaN</maxTime>
+			<matchType>MatchFromAndTo</matchType>
+			<intensityDetermination>0</intensityDetermination>
+			<centroidMatchTol>8</centroidMatchTol>
+			<centroidMatchTolInPpm>True</centroidMatchTolInPpm>
+			<centroidHalfWidth>35</centroidHalfWidth>
+			<centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
+			<valleyFactor>1.4</valleyFactor>
+			<isotopeValleyFactor>1.2</isotopeValleyFactor>
+			<advancedPeakSplitting>False</advancedPeakSplitting>
+			<intensityThreshold>0</intensityThreshold>
+			<labelMods>
+				<string/>
+			</labelMods>
+			<lcmsRunType>Reporter ion MS3</lcmsRunType>
+			<reQuantify>False</reQuantify>
+			<lfqMode>0</lfqMode>
+			<lfqSkipNorm>False</lfqSkipNorm>
+			<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
+			<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
+			<lfqMaxFeatures>100000</lfqMaxFeatures>
+			<neucodeMaxPpm>0</neucodeMaxPpm>
+			<neucodeResolution>0</neucodeResolution>
+			<neucodeResolutionInMda>False</neucodeResolutionInMda>
+			<neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
+			<fastLfq>True</fastLfq>
+			<lfqRestrictFeatures>False</lfqRestrictFeatures>
+			<lfqMinRatioCount>2</lfqMinRatioCount>
+			<maxLabeledAa>0</maxLabeledAa>
+			<maxNmods>5</maxNmods>
+			<maxMissedCleavages>2</maxMissedCleavages>
+			<multiplicity>1</multiplicity>
+			<enzymeMode>0</enzymeMode>
+			<complementaryReporterType>0</complementaryReporterType>
+			<reporterNormalization>0</reporterNormalization>
+			<neucodeIntensityMode>0</neucodeIntensityMode>
+			<fixedModifications/>
+			<enzymes>
+				<string>Trypsin/P</string>
+			</enzymes>
+			<enzymesFirstSearch>
+         </enzymesFirstSearch>
+			<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
+			<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
+			<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
+			<variableModifications>
+				<string>Oxidation (M)</string>
+			</variableModifications>
+			<useMultiModification>False</useMultiModification>
+			<multiModifications>
+         </multiModifications>
+			<isobaricLabels>
+				<IsobaricLabelInfo>
+					<internalLabel>TMT2plex-Lys126</internalLabel>
+					<terminalLabel>TMT2plex-Nter126</terminalLabel>
+					<correctionFactorM2>0</correctionFactorM2>
+					<correctionFactorM1>0</correctionFactorM1>
+					<correctionFactorP1>6.7</correctionFactorP1>
+					<correctionFactorP2>3</correctionFactorP2>
+					<tmtLike>True</tmtLike>
+				</IsobaricLabelInfo>
+				<IsobaricLabelInfo>
+					<internalLabel>TMT2plex-Lys127</internalLabel>
+					<terminalLabel>TMT2plex-Nter127</terminalLabel>
+					<correctionFactorM2>0</correctionFactorM2>
+					<correctionFactorM1>0</correctionFactorM1>
+					<correctionFactorP1>0</correctionFactorP1>
+					<correctionFactorP2>0</correctionFactorP2>
+					<tmtLike>True</tmtLike>
+				</IsobaricLabelInfo>
+			</isobaricLabels>
+			<neucodeLabels>
+         </neucodeLabels>
+			<variableModificationsFirstSearch>
+         </variableModificationsFirstSearch>
+			<hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
+			<additionalVariableModifications>
+         </additionalVariableModifications>
+			<additionalVariableModificationProteins>
+         </additionalVariableModificationProteins>
+			<doMassFiltering>True</doMassFiltering>
+			<firstSearchTol>20</firstSearchTol>
+			<mainSearchTol>4.5</mainSearchTol>
+			<searchTolInPpm>True</searchTolInPpm>
+			<isotopeMatchTol>2</isotopeMatchTol>
+			<isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
+			<isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
+			<theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
+			<checkMassDeficit>True</checkMassDeficit>
+			<recalibrationInPpm>True</recalibrationInPpm>
+			<intensityDependentCalibration>False</intensityDependentCalibration>
+			<minScoreForCalibration>70</minScoreForCalibration>
+			<matchLibraryFile>False</matchLibraryFile>
+			<libraryFile/>
+			<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
+			<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
+			<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
+			<reporterMassTolerance>0.003</reporterMassTolerance>
+			<reporterPif>0</reporterPif>
+			<filterPif>False</filterPif>
+			<reporterFraction>0</reporterFraction>
+			<reporterBasePeakRatio>0</reporterBasePeakRatio>
+			<timsHalfWidth>0</timsHalfWidth>
+			<timsStep>0</timsStep>
+			<timsResolution>0</timsResolution>
+			<timsMinMsmsIntensity>0</timsMinMsmsIntensity>
+			<timsRemovePrecursor>True</timsRemovePrecursor>
+			<timsIsobaricLabels>False</timsIsobaricLabels>
+			<timsCollapseMsms>True</timsCollapseMsms>
+			<crosslinkSearch>False</crosslinkSearch>
+			<crossLinker/>
+			<minMatchXl>0</minMatchXl>
+			<minPairedPepLenXl>6</minPairedPepLenXl>
+			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
+			<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
+			<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
+			<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
+			<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
+			<crosslinkModifications>
+         </crosslinkModifications>
+			<crosslinkFastaFiles>
+         </crosslinkFastaFiles>
+			<crosslinkSites>
+         </crosslinkSites>
+			<crosslinkNetworkFiles>
+         </crosslinkNetworkFiles>
+			<crosslinkMode/>
+			<peakRefinement>False</peakRefinement>
+			<isobaricSumOverWindow>True</isobaricSumOverWindow>
+			<isobaricWeightExponent>0.75</isobaricWeightExponent>
+			<diaLibraryType>0</diaLibraryType>
+			<diaLibraryPath/>
+			<diaPeptidePaths>
+         </diaPeptidePaths>
+			<diaEvidencePaths>
+         </diaEvidencePaths>
+			<diaMsmsPaths>
+         </diaMsmsPaths>
+			<diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
+			<diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
+			<diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
+			<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
+			<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
+			<diaScoreN>7</diaScoreN>
+			<diaMinScore>2.99</diaMinScore>
+			<diaPrecursorQuant>False</diaPrecursorQuant>
+			<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
+		</parameterGroup>
+		<parameterGroup>
+			<msInstrument>0</msInstrument>
+			<maxCharge>7</maxCharge>
+			<minPeakLen>2</minPeakLen>
+			<diaMinPeakLen>2</diaMinPeakLen>
+			<useMs1Centroids>False</useMs1Centroids>
+			<useMs2Centroids>False</useMs2Centroids>
+			<cutPeaks>True</cutPeaks>
+			<gapScans>1</gapScans>
+			<minTime>NaN</minTime>
+			<maxTime>NaN</maxTime>
+			<matchType>MatchFromAndTo</matchType>
+			<intensityDetermination>0</intensityDetermination>
+			<centroidMatchTol>8</centroidMatchTol>
+			<centroidMatchTolInPpm>True</centroidMatchTolInPpm>
+			<centroidHalfWidth>35</centroidHalfWidth>
+			<centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
+			<valleyFactor>1.4</valleyFactor>
+			<isotopeValleyFactor>1.2</isotopeValleyFactor>
+			<advancedPeakSplitting>False</advancedPeakSplitting>
+			<intensityThreshold>0</intensityThreshold>
+			<labelMods>
+				<string/>
+			</labelMods>
+			<lcmsRunType>Reporter ion MS3</lcmsRunType>
+			<reQuantify>False</reQuantify>
+			<lfqMode>0</lfqMode>
+			<lfqSkipNorm>False</lfqSkipNorm>
+			<lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
+			<lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
+			<lfqMaxFeatures>100000</lfqMaxFeatures>
+			<neucodeMaxPpm>0</neucodeMaxPpm>
+			<neucodeResolution>0</neucodeResolution>
+			<neucodeResolutionInMda>False</neucodeResolutionInMda>
+			<neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
+			<fastLfq>True</fastLfq>
+			<lfqRestrictFeatures>False</lfqRestrictFeatures>
+			<lfqMinRatioCount>2</lfqMinRatioCount>
+			<maxLabeledAa>0</maxLabeledAa>
+			<maxNmods>5</maxNmods>
+			<maxMissedCleavages>2</maxMissedCleavages>
+			<multiplicity>1</multiplicity>
+			<enzymeMode>0</enzymeMode>
+			<complementaryReporterType>0</complementaryReporterType>
+			<reporterNormalization>0</reporterNormalization>
+			<neucodeIntensityMode>0</neucodeIntensityMode>
+			<fixedModifications/>
+			<enzymes/>
+			<enzymesFirstSearch>
+         </enzymesFirstSearch>
+			<enzymeModeFirstSearch>0</enzymeModeFirstSearch>
+			<useEnzymeFirstSearch>False</useEnzymeFirstSearch>
+			<useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
+			<variableModifications/>
+			<useMultiModification>False</useMultiModification>
+			<multiModifications>
+         </multiModifications>
+			<isobaricLabels>
+				<IsobaricLabelInfo>
+					<internalLabel>iTRAQ4plex-Lys114</internalLabel>
+					<terminalLabel>iTRAQ4plex-Nter114</terminalLabel>
+					<correctionFactorM2>0</correctionFactorM2>
+					<correctionFactorM1>0</correctionFactorM1>
+					<correctionFactorP1>0</correctionFactorP1>
+					<correctionFactorP2>0</correctionFactorP2>
+					<tmtLike>False</tmtLike>
+				</IsobaricLabelInfo>
+				<IsobaricLabelInfo>
+					<internalLabel>iTRAQ4plex-Lys115</internalLabel>
+					<terminalLabel>iTRAQ4plex-Nter115</terminalLabel>
+					<correctionFactorM2>0</correctionFactorM2>
+					<correctionFactorM1>0</correctionFactorM1>
+					<correctionFactorP1>0</correctionFactorP1>
+					<correctionFactorP2>0</correctionFactorP2>
+					<tmtLike>False</tmtLike>
+				</IsobaricLabelInfo>
+				<IsobaricLabelInfo>
+					<internalLabel>iTRAQ4plex-Lys116</internalLabel>
+					<terminalLabel>iTRAQ4plex-Nter116</terminalLabel>
+					<correctionFactorM2>0</correctionFactorM2>
+					<correctionFactorM1>0</correctionFactorM1>
+					<correctionFactorP1>0</correctionFactorP1>
+					<correctionFactorP2>0</correctionFactorP2>
+					<tmtLike>False</tmtLike>
+				</IsobaricLabelInfo>
+				<IsobaricLabelInfo>
+					<internalLabel>iTRAQ4plex-Lys117</internalLabel>
+					<terminalLabel>iTRAQ4plex-Nter117</terminalLabel>
+					<correctionFactorM2>0</correctionFactorM2>
+					<correctionFactorM1>0</correctionFactorM1>
+					<correctionFactorP1>0</correctionFactorP1>
+					<correctionFactorP2>0</correctionFactorP2>
+					<tmtLike>False</tmtLike>
+				</IsobaricLabelInfo>
+			</isobaricLabels>
+			<neucodeLabels>
+         </neucodeLabels>
+			<variableModificationsFirstSearch>
+         </variableModificationsFirstSearch>
+			<hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
+			<additionalVariableModifications>
+         </additionalVariableModifications>
+			<additionalVariableModificationProteins>
+         </additionalVariableModificationProteins>
+			<doMassFiltering>True</doMassFiltering>
+			<firstSearchTol>20</firstSearchTol>
+			<mainSearchTol>4.5</mainSearchTol>
+			<searchTolInPpm>True</searchTolInPpm>
+			<isotopeMatchTol>2</isotopeMatchTol>
+			<isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
+			<isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
+			<theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
+			<checkMassDeficit>True</checkMassDeficit>
+			<recalibrationInPpm>True</recalibrationInPpm>
+			<intensityDependentCalibration>False</intensityDependentCalibration>
+			<minScoreForCalibration>70</minScoreForCalibration>
+			<matchLibraryFile>False</matchLibraryFile>
+			<libraryFile/>
+			<matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
+			<matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
+			<matchLabelTimeTolMin>0</matchLabelTimeTolMin>
+			<reporterMassTolerance>0.003</reporterMassTolerance>
+			<reporterPif>0.8</reporterPif>
+			<filterPif>True</filterPif>
+			<reporterFraction>0</reporterFraction>
+			<reporterBasePeakRatio>0</reporterBasePeakRatio>
+			<timsHalfWidth>0</timsHalfWidth>
+			<timsStep>0</timsStep>
+			<timsResolution>0</timsResolution>
+			<timsMinMsmsIntensity>0</timsMinMsmsIntensity>
+			<timsRemovePrecursor>True</timsRemovePrecursor>
+			<timsIsobaricLabels>False</timsIsobaricLabels>
+			<timsCollapseMsms>True</timsCollapseMsms>
+			<crosslinkSearch>False</crosslinkSearch>
+			<crossLinker/>
+			<minMatchXl>0</minMatchXl>
+			<minPairedPepLenXl>6</minPairedPepLenXl>
+			<crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
+			<crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
+			<crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
+			<crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
+			<crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
+			<crosslinkModifications>
+         </crosslinkModifications>
+			<crosslinkFastaFiles>
+         </crosslinkFastaFiles>
+			<crosslinkSites>
+         </crosslinkSites>
+			<crosslinkNetworkFiles>
+         </crosslinkNetworkFiles>
+			<crosslinkMode/>
+			<peakRefinement>False</peakRefinement>
+			<isobaricSumOverWindow>True</isobaricSumOverWindow>
+			<isobaricWeightExponent>0.75</isobaricWeightExponent>
+			<diaLibraryType>0</diaLibraryType>
+			<diaLibraryPath/>
+			<diaPeptidePaths>
+         </diaPeptidePaths>
+			<diaEvidencePaths>
+         </diaEvidencePaths>
+			<diaMsmsPaths>
+         </diaMsmsPaths>
+			<diaInitialPrecMassTolPpm>20</diaInitialPrecMassTolPpm>
+			<diaInitialFragMassTolPpm>20</diaInitialFragMassTolPpm>
+			<diaCorrThresholdFeatureClustering>0.85</diaCorrThresholdFeatureClustering>
+			<diaPrecTolPpmFeatureClustering>2</diaPrecTolPpmFeatureClustering>
+			<diaFragTolPpmFeatureClustering>2</diaFragTolPpmFeatureClustering>
+			<diaScoreN>7</diaScoreN>
+			<diaMinScore>2.99</diaMinScore>
+			<diaPrecursorQuant>False</diaPrecursorQuant>
+			<diaDiaTopNFragmentsForQuant>3</diaDiaTopNFragmentsForQuant>
+		</parameterGroup>
+	</parameterGroups>
+	<msmsParamsArray>
+		<msmsParams>
+			<Name>FTMS</Name>
+			<MatchTolerance>20</MatchTolerance>
+			<MatchToleranceInPpm>True</MatchToleranceInPpm>
+			<DeisotopeTolerance>7</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>10</DeNovoTolerance>
+			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
+			<Deisotope>True</Deisotope>
+			<Topx>12</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+		<msmsParams>
+			<Name>ITMS</Name>
+			<MatchTolerance>0.5</MatchTolerance>
+			<MatchToleranceInPpm>False</MatchToleranceInPpm>
+			<DeisotopeTolerance>0.15</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>0.25</DeNovoTolerance>
+			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+			<Deisotope>False</Deisotope>
+			<Topx>8</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+		<msmsParams>
+			<Name>TOF</Name>
+			<MatchTolerance>40</MatchTolerance>
+			<MatchToleranceInPpm>True</MatchToleranceInPpm>
+			<DeisotopeTolerance>0.01</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>False</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>0.02</DeNovoTolerance>
+			<DeNovoToleranceInPpm>False</DeNovoToleranceInPpm>
+			<Deisotope>True</Deisotope>
+			<Topx>10</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+		<msmsParams>
+			<Name>Unknown</Name>
+			<MatchTolerance>20</MatchTolerance>
+			<MatchToleranceInPpm>True</MatchToleranceInPpm>
+			<DeisotopeTolerance>7</DeisotopeTolerance>
+			<DeisotopeToleranceInPpm>True</DeisotopeToleranceInPpm>
+			<DeNovoTolerance>10</DeNovoTolerance>
+			<DeNovoToleranceInPpm>True</DeNovoToleranceInPpm>
+			<Deisotope>True</Deisotope>
+			<Topx>12</Topx>
+			<TopxInterval>100</TopxInterval>
+			<HigherCharges>True</HigherCharges>
+			<IncludeWater>True</IncludeWater>
+			<IncludeAmmonia>True</IncludeAmmonia>
+			<DependentLosses>True</DependentLosses>
+			<Recalibration>False</Recalibration>
+		</msmsParams>
+	</msmsParamsArray>
+	<fragmentationParamsArray>
+		<fragmentationParams>
+			<Name>CID</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>HCD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>ETD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>PQD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>ETHCD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>ETCID</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>UVPD</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+		<fragmentationParams>
+			<Name>Unknown</Name>
+			<Connected>False</Connected>
+			<ConnectedScore0>1</ConnectedScore0>
+			<ConnectedScore1>1</ConnectedScore1>
+			<ConnectedScore2>1</ConnectedScore2>
+			<InternalFragments>False</InternalFragments>
+			<InternalFragmentWeight>1</InternalFragmentWeight>
+			<InternalFragmentAas>KRH</InternalFragmentAas>
+		</fragmentationParams>
+	</fragmentationParamsArray>
+</MaxQuantParams>
+